Abstract

Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds throughout the genome of embryonic stem cells, with the majority of binding sites located at transcription start sites (TSSs) of CpG-rich promoters and within genes. The hmC modification is found in gene bodies and in contrast to mC is also enriched at CpG-rich TSSs. We provide evidence further that TET1 has a role in transcriptional repression. TET1 binds a significant proportion of Polycomb group target genes. Furthermore, TET1 associates and colocalizes with the SIN3A co-repressor complex. We propose that TET1 fine-tunes transcription, opposes aberrant DNA methylation at CpG-rich sequences and thereby contributes to the regulation of DNA methylation fidelity.

Knockdown of Tet1 in ES cells affects transcription.a, Microarray analyses were performed in control (shScr) and Tet1 knockdown cells (shTet1#4 and shTet1#5) in triplicates. Venn diagram showing overlap between TET1-bound genes, and genes up- or downregulated by both shRNAs using a cut-off of FDR < 0.05. b, qRT–PCR validation of selected genes. c, Genes that were found upregulated or downregulated by Tet1 knockdown show similar regulation in Dnmt TKO ES cells. All error bars denote s.d., n = 3.